菜单
Cluster and compare biosynthetic gene clusters across genomes with BiG-SCAPE (similarity networks of antiSMASH regions). Use after batch antiSMASH for BGC family discovery. Upstream: https://github.com/medema-group/BiG-SCAPE.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill bigscape命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
ABRicate — mass screening of contigs for AMR/virulence/plasmid markers against bundled databases (ResFinder, CARD, NCBI, VFDB, PlasmidFinder, EcoLI_VF, ARG-ANNOT, MEGARES, …). Use for fast multi-DB isolate or MAG screens and database concordance checks. Upstream: https://github.com/tseemann/abricate. Route via cge-finders / microbial-mining; official CGE CLI still via resfinder/plasmidfinder when phenotype mapping or PointFinder is required.
Route Center for Genomic Epidemiology (CGE) Finder-style screens and related isolate typing: PlasmidFinder, ResFinder, PointFinder, DisinFinder, VirulenceFinder, MobileElementFinder, pMLST, plus staramr / ABRicate wrappers and chromosomal mlst. Use for clinical/One-Health isolate typing and plasmid-borne AMR context — not community-wide dark-matter discovery. Child skills: plasmidfinder, resfinder, pointfinder, disinfinder, virulencefinder, mobileelementfinder, pmlst, staramr, abricate, mlst. Complements genomad, mob-suite, rgi, mobileog. Route via microbial-mining.
DisinFinder — CGE disinfectant / biocide resistance gene screen via the DisinFinder database, typically run through ResFinder. Use for isolate biocide-resistance markers alongside acquired AMR. DB: https://bitbucket.org/genomicepidemiology/disinfinder_db. Route via cge-finders / resfinder / microbial-mining.
基于 SOC 职业分类
正在显示 SKILL.md
| name | bigscape |
| description | Cluster and compare biosynthetic gene clusters across genomes with BiG-SCAPE (similarity networks of antiSMASH regions). Use after batch antiSMASH for BGC family discovery. Upstream: https://github.com/medema-group/BiG-SCAPE. |
| license | MIT |
| category | analysis-tools |
| tags | ["BGC","network","genome-mining","antiSMASH"] |
| upstream | https://github.com/medema-group/BiG-SCAPE |
| stage | mining |
Upstream: medema-group/BiG-SCAPE
Navarro-Muñoz, J. C. et al. A computational framework to explore large-scale biosynthetic diversity. Nat. Chem. Biol. 16, 60–68 (2020). https://doi.org/10.1038/s41589-019-0400-9
BiG-SCAPE groups antiSMASH regions into BGC families via similarity networks. Requires consistent antiSMASH outputs. Family membership ≠ identical chemistry — use for prioritization and diversity plots.
# After antiSMASH on many MAGs into a common input layout (see BiG-SCAPE docs):
bigscape -i temp/antismash_collection -o temp/bigscape -c 16 \
--mibig --include_gbk_dir
CLI flags evolve — verify with your BiG-SCAPE version help.
antismash · microbial-mining · bakta · visualization